The amplitude and phase fluctuations of A-scans, influenced by the galvanometer positioning accuracy, mechanical jitter, and especially the ovement of the sample, may lead to the distortion and degradation of the tissue structure images and the blood flow images within tissue beds in frequency domain optical coherence tomography. The amplitude registration method for A-scans is proposed based on the minimum intensity difference matching criterion, Lorentzian curve fitting method, and compensation of the optical path difference in interference spectrum. The phase differences between A-scans are detected and registered by matching of phase distribution characteristics of A-scans. After the amplitude and phase registration, the complex signal differences between two A-scans are calculated to eliminate the effect of the static tissue on the blood flow imaging. The eye scanning experiments were performed and three-dimensional blood flow images of retina were acquired. Experiment results indicate that the effect of system scanning accuracy and tissue movement on the image quality can be effectively eliminated by the proposed amplitude and phase registration method. The fast and accurate phase registration method can also be used in Doppler OCT, phase microscope, and other phase related applications.